After I successfully run the implementation phase from Project Navigator, then run the FPGA Editor from Project Navigator (not from the Windows menu system), the following warning appears:
"Warning: The design xxx.ncd is not up to date and may have been generated by a previous implementation run. Do you want to continue opening FPGA Editor on this out of date file?""
This issue occurs when PAR generates ".par" and ".ncd" files at the end of a successful Place and Route, but the Timestamp of the ".ncd" file is older than the ".par" file (usually by 1 second).
You can ignore the warning message if you know that the implementation is up-to-date.
This issue is resolved in ISE 11.1.